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Recent advances in remote sensing of solar-induced chlorophyll fluorescence (SIF) have improved the capabilities of monitoring large-scale Gross Primary Productivity (GPP). However, SIF observations are subject to directional effects which can lead to considerable uncertainties in various applications. Practical approaches for normalizing directional SIF observations to nadir viewing, to minimize the directional effects, have not been well studied. Here we developed two practical and physically-solid approaches for removing the directional effects of anisotropic SIF observations: one is based on near-infrared or red reflectance of vegetation (NIRv and Redv), and the other is based on the kernel-driven model with multi-angular SIF measurements. The first approach uses surface reflectance while the second approach directly leverages multi-angular SIF measurements. The performance of the two approaches was evaluated using a dataset of multi-angular measurements of SIF and reflectance collected with a high-resolution field spectrometer over different plant canopies. Results show that the relative mean absolute errors between the normalized nadir SIF and the observed SIF at nadir decrease by 3–6% (far-red) and 6–8% (red) for the first approach, and by 7–13% and 6–11% for the second approach, compared to the original data, respectively. The effectiveness and simplicity of our proposed approaches provide great potential to generate long-term and consistent SIF data records with minimized directional effects.

Plant functional diversity, defined as the range of plant chemical, physiological and structural properties within plants, is a key component of biodiversity which controls the ecosystem functioning and stability. Monitoring its variations across space and over time is critical in ecological studies. So far, several reflectance-based metrics have been tested to achieve this objective, yielding different degrees of success. Our work aimed at exploring the potential of a novel metric based on far-red sun-induced chlorophyll fluorescence (F760) to map the functional diversity of terrestrial ecosystems. This was achieved exploiting high-resolution images collected over a mixed forest ecosystem with the HyPlant sensor, deployed as an airborne demonstrator of the forthcoming ESA-FLEX satellite. A reference functional diversity map was obtained applying the Rao's Q entropy metric on principal components calculated on key plant functional trait maps retrieved from the hyperspectral reflectance cube. Based on the spectral variation hypothesis, which states that the biodiversity signal is encoded in the spectral heterogeneity, two moving window-based approaches were tested to estimate the functional diversity from continuous spectral data: i) the Rao's Q entropy metric calculated on the normalized difference vegetation index (NDVI) and ii) the coefficient of variation (CV) calculated on hyperspectral reflectance. Finally, a third moving window approach was used to estimate the functional diversity based on F760 heterogeneity quantified through the calculation of the Rao's Q entropy metric. Results showed a strong underestimation of the functional diversity using the Rao's Q index based on NDVI and the CV of reflectance. In both cases, a weak correlation was found against the reference functional diversity map (r2 = 0.05, p < .001 and r2 = 0.04, p < .001, respectively). Conversely, the Rao's Q index calculated on F760 revealed similar patterns as the ones observed in the reference map and a better correlation (r2 = 0.5, p < .001). This corroborates the potential of far-red F for assessing the functional diversity of terrestrial eco- systems, opening unprecedented perspectives for biodiversity monitoring across different spatial and temporal scales.

The increasing amount of continuous time series of solar-induced fluorescence (SIF) and vegetation indices (e.g. Photochemical Reflectance Index, PRI) acquired with high temporal (sub-minute) frequencies is foreseen to allow tracking of the structural and physiological changes of vegetation in a variety of ecosystems. Coupled with observations of CO2, water, and energy fluxes from eddy covariance flux towers, these measurements can bring new insights into the remote monitoring of ecosystem functioning. However, continuously changing solar-view geometry imposes directional effects on diurnal cycles of the fluorescence radiance in the observation direction (F) and PRI, controlled by structural and biochemical vegetation properties. An improved understanding of these variations can potentially help to disentangle directional responses of vegetation from physiological ones in the continuous long-term optical measurements and, therefore, allow to deconvolve the physiological information relevant to ecosystem functioning. Moreover, this will also be useful for better interpreting and validating F and PRI satellite products (e.g., from the upcoming ESA FLEX mission). Many previous studies focused on the characterization of reflectance directionality, but only a handful of studies investigated directional effects on F and vegetation indices related to plant physiology. The aim of this study is to contribute to the understanding of red (F687) and far-red (F760) fluorescence and PRI anisotropy based on field spectroscopy data and simulations with the Soil-Canopy Observation of Photochemistry and Energy fluxes (SCOPE) model. We present an extensive dataset of multi-angular measurements of F and PRI collected at canopy level with a high-resolution instrument (FloX, JB Hyperspectral Devices UG, Germany) over different ecosystems: Mediterranean grassland, alfalfa, chickpea and rice. We found, that F760 and F687 directional responses of horizontally homogeneous canopies are characterized by higher values in the backscatter direction with a maximum in the hotspot and lower values in the forward scatter direction. The PRI exhibited similar response due to its sensitivity to sunlit-shaded canopy fractions. As confirmed by radiative transfer forward simulations, we show that in the field measurements leaf inclination distribution function controls the shape of F and PRI anisotropic response (bowl-like/dome-like shapes), while leaf area index and the ratio of leaf width to canopy height affect the magnitude and the width of the hotspot. Finally, we discuss the implications of off-nadir viewing geometry for continuous ground measurements. F observations under oblique viewing angles showed up to 67 % difference compared to nadir observations, therefore, we suggest maintaining nadir viewing geometry for continuous measurements of F and vegetation indices. Alternatively, a correction scheme should be developed and tested against multi-angular measurements to properly account for anisotropy of canopy F and PRI observations. The quantitative characterization of these effects in varying illumination geometries for different canopies that was performed in this study will also be useful for the validation of remote sensing F and PRI products at different spatial and temporal scales.

Retrieval of Sun-Induced Chlorophyll Fluorescence (F) spectrum is one of the challenging perspectives for further advancing F studies towards a better characterization of vegetation structure and functioning. In this study, a simplified Spectral Fitting retrieval algorithm suitable for retrieving the F spectrum with a limited number of parameters is proposed (two parameters for F). The novel algorithm is developed and tested on a set of radiative transfer simulations obtained by coupling SCOPE and MODTRAN5 codes, considering different chlorophyll content, leaf area index and noise levels to produce a large variability in fluorescence and reflectance spectra. The retrieval accuracy is quantified based on several metrics derived from the F spectrum (i.e., red and far-red peaks, O2 bands and spectrally-integrated values). Further, the algorithm is employed to process experimental field spectroscopy measurements collected over different crops during a long-lasting field campaign. The reliability of the retrieval algorithm on experimental measurements is evaluated by cross-comparison with F values computed by an independent retrieval method (i.e., SFM at O2 bands). For the first time, the evolution of the F spectrum along the entire growing season for a forage crop is analyzed and three diverse F spectra are identified at different growing stages. The results show that red F is larger for young canopy; while red and far-red F have similar intensity in an intermediate stage; finally, far-red F is significantly larger for the rest of the season.

[EN] The interest of the scientific community on the remote observation of sun-induced chlorophyll fluorescence (SIF) has increased in the recent years. In this context, hyperspectral ground measurements play a crucial role in the calibration and validation of future satellite missions. For this reason, the European cooperation in science and technology (COST) Action ES1309 OPTIMISE has compiled three papers on instrument characterization, measurement setups and protocols, and retrieval methods (current paper). This study is divided in two sections; first, we evaluated the uncertainties in SIF retrieval methods (e.g., Fraunhofer line depth (FLD) approaches and spectral fitting method (SFM)) for a combination of off-the-shelf commercial spectrometers. Secondly, we evaluated how an erroneous implementation of the retrieval methods increases the uncertainty in the estimated SIF values. Results show that the SFM approach applied to high-resolution spectra provided the most reliable SIF retrieval with a relative error (RE) 6% and, This article is based upon work from COST Action ES1309 OPTIMISE, supported by COST (European Cooperation in Science and Technology; www.cost.eu).Cendrero-Mateo M.P. and Alonso L. are currently funded by AVANFLEX project (Advanced Products for the FLEX mission), no ESP2016-79503-C2-1-P, Ministry of Economy and Competitiveness, Spain. Wieneke S. is currently funded by the individual fellowship of the European Union's H2020 Marie Sklodowska-Curie actions under the grant agreement ReSPEc no [795299]. Goulas Y. is currently funded by the ECOFLUO project (In-situ Remote Sensing of Chlorophyll Fluorescence to Monitor Carbon Dynamics in Ecosystems in support of the FLEX mission), no 4500058116 and 4500058229, Centre National d'Etudes Spatiales (CNES), France. Mac Arthur, A. was funded by the UK's NERC/NCEO Field Spectroscopy Facility, at the University of Edinburgh. Pacheco-Labrador, J. was supported by the EnMAP project MoReDEHESHyReS "Modelling Responses of Dehesas with Hyperspectral Remote Sensing" (Contract No. 50EE1621, German Aerospace Center (DLR) and the German Federal Ministry of Economic Affairs and Energy) and the Alexander von Humboldt Foundation via Max-Planck Prize to Markus Reichstein.

Compact multi-spectral sensors that can be mounted on lightweight drones are now widely available and applied within the geo- and environmental sciences. However; the spatial consistency and radiometric quality of data from such sensors is relatively poorly explored beyond the lab; in operational settings and against other sensors. This study explores the extent to which accurate hemispherical-conical reflectance factors (HCRF) and vegetation indices (specifically: normalised difference vegetation index (NDVI) and chlorophyll red-edge index (CHL)) can be derived from a low-cost multispectral drone-mounted sensor (Parrot Sequoia). The drone datasets were assessed using reference panels and a high quality 1 m resolution reference dataset collected near-simultaneously by an airborne imaging spectrometer (HyPlant). Relative errors relating to the radiometric calibration to HCRF values were in the 4 to 15% range whereas deviations assessed for a maize field case study were larger (5 to 28%). Drone-derived vegetation indices showed relatively good agreement for NDVI with both HyPlant and Sentinel 2 products (R2 = 0.91). The HCRF; NDVI and CHL products from the Sequoia showed bias for high and low reflective surfaces. The spatial consistency of the products was high with minimal view angle effects in visible bands. In summary; compact multi-spectral sensors such as the Parrot Sequoia show good potential for use in index-based vegetation monitoring studies across scales but care must be taken when assuming derived HCRF to represent the true optical properties of the imaged surface.

The contribution presents the development and testing of a fluorescence retrieval scheme based on the ESA's FLuorescence EXplorer mission concept. The algorithm employs on a coupled surface-atmosphere forward model at oxygen absorption bands: i) the atmospheric effect is computed by MODTRAN5; ii) the surface reflectance and fluorescence are modeled by means of the Spectral Fitting approach. The algorithm, previously tested on numerical simulations, was further implemented and optimized to process real observations collected by the FLEX airborne demonstrator HyPlant. The retrieval scheme has been tested on a number of flight lines collected in several locations, different ecosystems types, atmospheric conditions and instrument observation conditions. For the first time, this work shows the capability of retrieving canopy fluorescence from real airborne observations by means of a physically-based algorithm as envisaged for FLEX. The results achieved on the large core data sets of imageries show the consistency of the physical retrieval algorithm for a wide range of scenarios and fluorescence values are in line with ground observations.

Leaf fluorescence can be used to track plant development and stress, and is considered the most direct measurement of photosynthetic activity available from remote sensing techniques. Red and far-red Sun Induced chlorophyll Fluorescence (SIF) maps were generated from high spatial resolution images collected with the HyPlant airborne spectrometer over even-aged loblolly pine plantations in North Carolina (USA). Canopy fluorescence yield (i.e., the fluorescence flux normalized by the light absorbed) in the red and far-red peaks was computed. This quantifies the fluorescence emission efficiencies that is more directly linked to canopy function compared to SIF radiances. Fluorescence fluxes and yields were investigated in relation to tree age to infer new insights on the potential of those measurements in better describing ecosystem processes. The results showed that red fluorescence yield varies with stand age. Young stands exhibited a nearly 2-fold higher red fluorescence yield than mature forest plantations, while the far-red fluorescence yield remained constant. We interpreted this finding in a context of photosynthetic stomatal limitation in aging loblolly pine stands. Current and future satellite missions provide global datasets of SIF at coarse spatial resolution, resulting in intra-pixel mixture effects, which could be a confounding factor for fluorescence signal interpretation. To mitigate this effect, we propose a surrogate of the fluorescence yield, namely the Canopy Cover Fluorescence Index (CCFI) that accounts for the spatial variability in canopy structure by exploiting the vegetation fractional cover. It was found that spatial aggregation tended to mask the effective relationships, while the CCFI was still able to maintain this link. This study is a first attempt in interpreting the fluorescence variability in aging forest stands and it may open new perspectives in understanding long-term forest dynamics in response to future climatic conditions from remote sensing of SIF. This article is protected by copyright. All rights reserved

Sun-induced canopy chlorophyll fluorescence in both the red (FR) and far-red (FFR) regions was estimated across a range of temporal scales and a range of species from different plant functional types using high resolution radiance spectra collected on the ground. Field measurements were collected with a state-of-the-art spectrometer setup and standardized methodology. Results showed that different plant species were characterized by different fluorescence magnitude. In general, the highest fluorescence emissions were measured in crops followed by broadleaf and then needleleaf species. Red fluorescence values were generally lower than those measured in the far-red region due to the reabsorption of FR by photosynthetic pigments within the canopy layers. Canopy chlorophyll fluorescence was related to plant photosynthetic capacity, but also varied according to leaf and canopy characteristics, such as leaf chlorophyll concentration and Leaf Area Index (LAI). Results gathered from field measurements were compared to radiative transfer model simulations with the Soil-Canopy Observation of Photochemistry and Energy fluxes (SCOPE) model. Overall, simulation results confirmed a major contribution of leaf chlorophyll concentration and LAI to the fluorescence signal. However, some discrepancies between simulated and experimental data were found in broadleaf species. These discrepancies may be explained by uncertainties in individual species LAI estimation in mixed forests or by the effect of other model parameters and/or model representation errors. This is the first study showing sun-induced fluorescence experimental data on the variations in the two emission regions and providing quantitative information about the absolute magnitude of fluorescence emission from a range of vegetation types.